Variant report

Variant	rs6719174
Chromosome Location	chr2:47402870-47402871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr2:47402668-47403287	K562	blood:	n/a	chr2:47403092-47403106 chr2:47402818-47402829 chr2:47402924-47402938
2	POLR2A	chr2:47400066-47404709	MCF10A-Er-Src	breast:	n/a	n/a
3	RCOR1	chr2:47402446-47404311	HepG2	liver:	n/a	n/a
4	CHD2	chr2:47401947-47404355	Hela-S3	cervix:	n/a	chr2:47402298-47402308 chr2:47403103-47403113 chr2:47403143-47403150
5	RAD21	chr2:47396737-47406140	SK-N-SH	brain:	n/a	chr2:47402878-47402891 chr2:47402875-47402894 chr2:47403663-47403673 chr2:47403109-47403119 chr2:47406082-47406094
6	POLR2A	chr2:47402360-47404590	GM19193	blood:	n/a	n/a
7	REST	chr2:47402702-47403251	K562	blood:	n/a	chr2:47402851-47402871 chr2:47402862-47402882 chr2:47402862-47402882 chr2:47402851-47402871
8	CREB1	chr2:47402699-47404553	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:47401635-47404602	U87	brain:	n/a	n/a
10	BCLAF1	chr2:47401872-47402871	GM12878	blood:	n/a	n/a
11	PBX3	chr2:47402752-47404459	SK-N-SH	brain:	n/a	chr2:47403950-47403970 chr2:47403286-47403295 chr2:47403969-47403978
12	MYC	chr2:47402835-47404240	MCF-7	breast:	n/a	chr2:47403119-47403128
13	TAF1	chr2:47402688-47404507	ECC-1	luminal epithelium:	n/a	n/a
14	ZNF263	chr2:47401891-47404452	HEK293-T-REx	kidney:	n/a	chr2:47402297-47402306
15	POLR2A	chr2:47401654-47404707	GM12892	blood:	n/a	n/a
16	CREB1	chr2:47402700-47404332	A549	lung:	n/a	n/a
17	MAX	chr2:47402580-47404468	SK-N-SH	brain:	n/a	chr2:47403119-47403128
18	POLR2A	chr2:47396007-47404625	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr2:47382524-47406811	PFSK-1	brain:	n/a	n/a
20	GATA2	chr2:47402404-47404535	SH-SY5Y	brain:	n/a	chr2:47403316-47403324 chr2:47402775-47402788
21	TBL1XR1	chr2:47401993-47404757	K562	blood:	n/a	n/a
22	CTCF	chr2:47402760-47402910	WERI-Rb-1	eye:	n/a	chr2:47402877-47402890 chr2:47402877-47402885
23	POLR2A	chr2:47401945-47404470	H1-neurons	neurons:	n/a	n/a
24	POLR2A	chr2:47402795-47403770	A549	lung:	n/a	n/a
25	SIN3AK20	chr2:47401971-47403281	K562	blood:	n/a	n/a
26	EGR1	chr2:47402645-47403206	K562	blood:	n/a	chr2:47402821-47402834 chr2:47402957-47402971
27	CHD2	chr2:47402261-47404399	K562	blood:	n/a	chr2:47402298-47402308 chr2:47403103-47403113 chr2:47403143-47403150
28	MXI1	chr2:47400996-47405178	IMR90	lung:	n/a	chr2:47404059-47404074
29	CEBPD	chr2:47402509-47404628	K562	blood:	n/a	n/a
30	MYC	chr2:47402809-47404219	Hela-S3	cervix:	n/a	chr2:47403119-47403128
31	BHLHE40	chr2:47402754-47404431	HepG2	liver:	n/a	chr2:47402921-47402937
32	PML	chr2:47402514-47404394	K562	blood:	n/a	n/a
33	MAX	chr2:47401722-47404739	A549	lung:	n/a	chr2:47403119-47403128
34	POLR2A	chr2:47382225-47405286	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr2:47399144-47404652	GM12892	blood:	n/a	n/a
36	POLR2A	chr2:47402731-47404384	MCF-7	breast:	n/a	n/a
37	CREB1	chr2:47402508-47404645	HepG2	liver:	n/a	n/a
38	RAD21	chr2:47402820-47402922	K562	blood:	n/a	chr2:47402878-47402891 chr2:47402875-47402894
39	POLR2A	chr2:47401906-47403826	H1-hESC	embryonic stem cell:	n/a	n/a
40	CHD1	chr2:47401710-47402886	H1-hESC	embryonic stem cell:	n/a	chr2:47402298-47402308
41	MYC	chr2:47402663-47404503	K562	blood:	n/a	chr2:47403119-47403128
42	CTCF	chr2:47402780-47402930	HMEC	breast:	n/a	chr2:47402877-47402890 chr2:47402877-47402885
43	MAX	chr2:47402754-47404496	SK-N-SH	brain:	n/a	chr2:47403119-47403128
44	RAD21	chr2:47402737-47403149	K562	blood:	n/a	chr2:47402878-47402891 chr2:47402875-47402894 chr2:47403109-47403119
45	CTCF	chr2:47402760-47402910	SAEC	small airway:	n/a	chr2:47402877-47402890 chr2:47402877-47402885
46	POLR2A	chr2:47401709-47404696	GM12891	blood:	n/a	n/a
47	POLR2A	chr2:47402386-47404360	K562	blood:	n/a	n/a
48	TBP	chr2:47402675-47404304	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr2:47401967-47404465	HL-60	blood:	n/a	n/a
50	TEAD4	chr2:47401977-47402980	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:56966477..56967140-chr2:47402528..47403397,2	Hela-S3	cervix:
2	chr2:47402779..47405652-chr2:47594724..47597829,3	K562	blood:
3	chr2:47220862..47225029-chr2:47401840..47405113,4	K562	blood:
4	chr19:13262402..13265280-chr2:47401781..47403940,2	MCF-7	breast:
5	chr2:47399756..47406251-chr2:47447036..47455846,12	MCF-7	breast:
6	chr2:47402805..47405145-chr2:85764974..85766648,2	K562	blood:
7	chr2:46655601..46658738-chr2:47401405..47405423,5	K562	blood:
8	chr2:47141013..47143779-chr2:47401317..47404567,3	MCF-7	breast:
9	chr2:47140015..47142222-chr2:47401259..47403402,2	K562	blood:
10	chr2:47399705..47406684-chr2:47448496..47456698,16	K562	blood:
11	chr2:47319263..47321781-chr2:47402053..47403582,2	MCF-7	breast:
12	chr2:47166915..47170495-chr2:47399445..47404516,7	MCF-7	breast:
13	chr2:47205093..47209059-chr2:47402217..47405792,6	K562	blood:
14	chr2:47166107..47171055-chr2:47402078..47404965,9	K562	blood:
15	chr2:47402214..47404351-chr2:47556538..47558754,3	K562	blood:
16	chr2:47266621..47268333-chr2:47402251..47405072,2	K562	blood:
17	chr2:47402494..47404351-chr2:47556538..47558473,2	K562	blood:
18	chr16:31191454..31192007-chr2:47402830..47403555,2	Hela-S3	cervix:
19	chr2:47252232..47263251-chr2:47397787..47406051,20	MCF-7	breast:
20	chr2:47402569..47404558-chr6:27113813..27116617,2	K562	blood:
21	chr2:47400478..47403818-chr2:48008752..48011597,4	K562	blood:
22	chr2:47232895..47237077-chr2:47401374..47404385,4	MCF-7	breast:
23	chr1:28835371..28837619-chr2:47401530..47403667,2	K562	blood:
24	chr16:3022787..3025377-chr2:47401877..47403851,2	K562	blood:
25	chr1:45186357..45188685-chr2:47401476..47403610,2	K562	blood:
26	chr2:47399705..47405092-chr2:47450546..47458227,19	K562	blood:
27	chr2:47401421..47404385-chr2:47596204..47598281,3	MCF-7	breast:
28	chr2:47402571..47403290-chr2:47539949..47540802,2	MCF-7	breast:
29	chr2:47381115..47385095-chr2:47400722..47404896,4	MCF-7	breast:
30	chr2:47402764..47405389-chr2:47627574..47630501,3	K562	blood:
31	chr2:47401987..47404848-chr2:47628320..47632624,5	MCF-7	breast:
32	chr2:47168040..47171171-chr2:47402063..47404163,4	K562	blood:
33	chr2:47401904..47404708-chr2:47598417..47601115,2	MCF-7	breast:
34	chr2:47401510..47404292-chr3:9438426..9440104,2	K562	blood:
35	chr2:47260087..47265958-chr2:47400378..47404964,8	K562	blood:
36	chr2:38975839..38978922-chr2:47400598..47403972,4	K562	blood:
37	chr2:47135391..47138863-chr2:47402066..47404895,3	K562	blood:
38	chr2:38977033..38979904-chr2:47402717..47404547,2	K562	blood:
39	chr12:120728581..120730785-chr2:47402296..47404472,2	K562	blood:
40	chr2:47220711..47222484-chr2:47400487..47403204,2	MCF-7	breast:
41	chr2:47166485..47169114-chr2:47402596..47405123,4	MCF-7	breast:
42	chr2:47140743..47148534-chr2:47401019..47406419,10	MCF-7	breast:
43	chr2:47334355..47336509-chr2:47402555..47405238,2	MCF-7	breast:
44	chr2:47205588..47209510-chr2:47401817..47405792,7	K562	blood:
45	chr2:47142780..47146808-chr2:47401206..47405117,7	K562	blood:

Variant related genes	Relation type
CALM2	TF binding region
ENSG00000127564	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000051108	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000168137	Chromatin interaction
ENSG00000160888	Chromatin interaction
ENSG00000206573	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000187600	Chromatin interaction
ENSG00000267598	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000116062	Chromatin interaction
ENSG00000226087	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000236824	Chromatin interaction
ENSG00000239605	Chromatin interaction
ENSG00000095002	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000119888	Chromatin interaction
ENSG00000233845	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000180198	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11842	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4953472	0.86[AFR][1000 genomes]
rs56875665	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv457374	chr2:47313624-47448865	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv581754	chr2:47313624-47448865	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47399200-47404400	Active TSS	HSMMtube	muscle
2	chr2:47399800-47404200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:47399800-47404400	Active TSS	Stomach Smooth Muscle	stomach
4	chr2:47400000-47403000	Active TSS	Right Atrium	heart
5	chr2:47400000-47404000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:47400000-47404600	Active TSS	Psoas Muscle	Psoas
7	chr2:47400400-47405200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:47400600-47404600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr2:47400800-47403200	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr2:47400800-47404000	Active TSS	NH-A	brain
11	chr2:47400800-47404400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr2:47400800-47404400	Active TSS	Fetal Intestine Small	intestine
13	chr2:47400800-47404400	Active TSS	Ovary	ovary
14	chr2:47401000-47403200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:47401000-47403400	Active TSS	Aorta	Aorta
16	chr2:47401000-47404000	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:47401000-47404000	Active TSS	HMEC	breast
18	chr2:47401000-47404200	Active TSS	H1 Cell Line	embryonic stem cell
19	chr2:47401000-47404200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:47401000-47404200	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr2:47401000-47404200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:47401000-47404200	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr2:47401000-47404200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:47401000-47404200	Active TSS	Duodenum Mucosa	Duodenum
25	chr2:47401000-47404200	Active TSS	Fetal Intestine Large	intestine
26	chr2:47401000-47404200	Active TSS	Rectal Smooth Muscle	rectum
27	chr2:47401000-47404200	Active TSS	NHDF-Ad	bronchial
28	chr2:47401000-47404400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:47401000-47404400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:47401000-47404400	Active TSS	Brain Anterior Caudate	brain
31	chr2:47401000-47404400	Active TSS	Brain Hippocampus Middle	brain
32	chr2:47401000-47404400	Active TSS	Fetal Brain Female	brain
33	chr2:47401000-47404400	Active TSS	Fetal Kidney	kidney
34	chr2:47401000-47404400	Active TSS	GM12878-XiMat	blood
35	chr2:47401000-47404600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:47401000-47404600	Active TSS	Right Ventricle	heart
37	chr2:47401200-47404000	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr2:47401200-47404200	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr2:47401200-47404200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:47401200-47404200	Active TSS	Brain Angular Gyrus	brain
41	chr2:47401200-47404200	Active TSS	Brain Cingulate Gyrus	brain
42	chr2:47401200-47404200	Active TSS	NHLF	lung
43	chr2:47401200-47404400	Active TSS	Fetal Stomach	stomach
44	chr2:47401200-47404400	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr2:47401200-47404600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr2:47401200-47404600	Active TSS	Brain Substantia Nigra	brain
47	chr2:47401200-47404600	Active TSS	Colon Smooth Muscle	Colon
48	chr2:47401400-47403200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:47401400-47404000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:47401400-47404200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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